I have been trying to recreate the Battle Master Maneuvers section in my Homebrew Subclass. I can add the Feature Options and select them in the same way as long I make sure to set it up exactly the same as Battle Master. But if I try to add an option and check off the "Is Granted" the option seems to disappear on the sheet and wont show up anywhere except the Homebrew edit screens.

Is there a way to set it up that the Character will automatically gain the options I want without having to manually select them as they level?

Sort of. Don't use options, just make the feature grant you the action at the necessary level.

Hello! The "Is Granted" option is intended to work with an option that requires a previous option to qualify. This option will remove the option from being selected in the character builder, and if the character qualifies based on the pre-requisite option, it will appear on the character sheet. 

If you are trying to create an option like this, with an earlier option pre-requisite, this can do as you're looking for-- Share the homebrew link here and I can take a look to try and help you through it.

If you are not trying to create a chained option like this, "Is Granted" would not be the option you're looking for.

Hope that helps!